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ataudt / aneufinder

Find CNVs in single cell sequencing data.
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connect to host 4 port 22: Invalid argument #1

Closed leon8889 closed 7 years ago

leon8889 commented 8 years ago

I am trying to run Aneufinder(inputfolder=infolder, outputfolder=outfolder,format="bam", numCPU=cpu, method=c("HMM","dnacopy"),pairedEndReads = TRUE )

A config file is created and then I get the Message: Setting up parallel execution with 4 CPUs ...ssh: connect to host 4 port 22: Invalid argument and then nothing happens.

What is wrong here??

ataudt commented 8 years ago

Hi Leon,

I can reproduce your error by running Aneufinder(..., numCPU="4")

The correct way to run it is Aneufinder(..., numCPU=4)

Your variable 'cpu' most likely contains 4 as a string, not a number. Running Aneufinder(..., numCPU=as.numeric(cpu)) should fix the issue.

Best, Aaron

Dipl. Biol. (t.o.) Aaron Taudt | PhD Student | University Medical Center Groningen European Research Institute for the Biology of Ageing (ERIBA) | Quantitative Epigenetics A. Deusinglaan 1, gebouw 3226 | 9700 AD Groningen. | www.ERIBA.umcg.nlhttps://mail.umcg.nl/owa/UrlBlockedError.aspx

From: leon8889 [notifications@github.com] Sent: Tuesday, August 09, 2016 4:36 PM To: ataudt/aneufinder Subject: [ataudt/aneufinder] connect to host 4 port 22: Invalid argument (#1)

I am trying to run Aneufinder(inputfolder=infolder, outputfolder=outfolder,format="bam", numCPU=cpu, method=c("HMM","dnacopy"),pairedEndReads = TRUE )

A config file is created and then I get the Message: Setting up parallel execution with 4 CPUs ...ssh: connect to host 4 port 22: Invalid argument and then nothing happens.

What is wrong here??

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